To determine the prevalence of human papillomavirus (HPV) genotypes 6, 11, 16, 18, and 31 in Mexican women living in rural areas of Puebla, Mexico and to evaluate risk factors associated with cervical neoplasm in this population. A cross-sectional study was conducted in 326 women at the General Hospital of Metepec, Puebla. Cervical samples were obtained using a cytobrush and tested for HPV genotypes by PCR assays using type-specific primers. A questionnaire was completed regarding gynecological, obstetric, and sexual behavior of the patients. The overall prevalence of HPV infection was 25.4%, with two peaks of higher HPV prevalence in those aged 18-24 and 55-64 years. The individual genotype prevalences were: 9.6% HPV6, 4.8% HPV11, 54.2% HPV16, 37.3% HPV18, and 9.6% HPV31. Number of pregnancies was the most important risk factor associated with cervical cancer. HPV16 was the most common type found in all cervical lesions. Genotype 16 or 18 was detected in patients with a diagnosis of cervical cancer. We found two peaks of age-specific HPV prevalence similar to findings reported worldwide.